Certificat(s)

Team

No website documented

Annual visits:

36 000 an

Unique visits:

3 600 an

Quotes:

150

Latest update:

03-01-2015

Norine

Description

Norine is a public computational resource with a web interface and REST access to a knowledge-base of
nonribosomal peptides. It also contains dedicated tools : 2D graph viewer and editor, comparison of NRPs,
MyNorine, a tool allowing anybody to easly submit new nonribosomal peptides, Smiles2monomers (s2m), a
tool that deciphers the monomeric structure of polymers from their chemical structure.

Access conditions

No website documented

Annual visits:

Not documented

Unique visits:

Not documented

Quotes:

21

Downloads:

100

CRAC

Description

CRAC proposes a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a single step. CRAC uses a double k-mer profiling approach to detect candidate mutations, indels, splice or fusion junctions in each single read.

Access conditions

CRAC is released under a CECiLL licence (a GPL-compliant licence). You can download it and install it on your server.

No website documented

Annual visits:

4 848 an

Unique visits:

11 633 an

Quotes:

4

Downloads:

Not documented

RNAspace

Description

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.
RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs. RNAspace also allows to export putative RNAs in various formats.

Access conditions

RNAspace is an open source project. It is developed in Python. It is copyrighted with the GNU General Public License, and is free (in the GNU sense) for all to use, and is in constant development. RNAspace is hosted at Sourceforge. It is also available as a web server at rnaspace.org.

No website documented

Annual visits:

Not documented

Unique visits:

Not documented

Quotes:

10

Downloads:

Not documented

Vidjil

Description

Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes. V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated Rep-Seq methods and software.

Vidjil contains a high-throughput algorithm extracting V(D)J junctions and gather them into clones. This analysis is based on a seed heuristics and is fast and scalable, as, in the first phase, no alignment is performed with database germline sequences. Vidjil also contains a dynamic browser and a patient database for visualization and analysis of clones and their tracking along the time in a MRD setup or in a immunological study.

Access conditions

Vidjil is open-source, released under GNU GPLv3 license. You are welcome to redistribute it under certain conditions. This software is for research use only and comes with no warranty.

The browser can be accessed at rbx.vidjil.org/browser. The development code of Vidjil is available on GitHub, and the command-line version of Vidjil can also be downloaded below.

No website documented

Annual visits:

Not documented

Unique visits:

Not documented

Quotes:

53

Downloads:

Not documented

SortMeRNA

Description

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).

SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

Access conditions

SortMeRNA is implemented in C++ and freely distributed under the GNU lesser general public license (LGPL).

No website documented

Annual visits:

Not documented

Unique visits:

Not documented

Quotes:

Not documented

Downloads:

Not documented

miRkwood

Description

miRkwood is a web application that allows for the fast and easy identification of microRNAs. It is specifically designed for plant microRNAs.

Access conditions

miRkwood offers an user-friendly interface to navigate in the data, as well as many export options to allow the user to conduct further analyses on a local computer.

No website documented

Annual visits:

Not documented

Unique visits:

Not documented

Quotes:

90

Downloads:

Not documented

Carnac

Description

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

Access conditions

You can use Carnac via the web interface. It is also possible to download and install it locally (carnac.tar.gz and read_me). You need a C compiler.
A Windows executable is also available in this zip archive .